8C8C

Crystal Structure of Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (PI5P4Ka) bound to an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.216 

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Literature

Identification of ARUK2002821 as an isoform-selective PI5P4K alpha inhibitor.

Willems, H.M.G.Edwards, S.Boffey, H.K.Chawner, S.J.Green, C.Romero, T.Winpenny, D.Skidmore, J.Clarke, J.H.Andrews, S.P.

(2023) RSC Med Chem 14: 934-946

  • DOI: https://doi.org/10.1039/d3md00039g
  • Primary Citation of Related Structures:  
    8C8C

  • PubMed Abstract: 

    The phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) play a central role in regulating cell signalling pathways and, as such, have become therapeutic targets for diseases such as cancer, neurodegeneration and immunological disorders. Many of the PI5P4Kα inhibitors that have been reported to date have suffered from poor selectivity and/or potency and the availability of better tool molecules would facilitate biological exploration. Herein we report a novel PI5P4Kα inhibitor chemotype that was identified through virtual screening. The series was optimised to deliver ARUK2002821 (36), a potent PI5P4Kα inhibitor (pIC 50 = 8.0) which is selective vs. other PI5P4K isoforms and has broad selectivity against lipid and protein kinases. ADMET and target engagement data are provided for this tool molecule and others in the series, as well as an X-ray structure of 36 solved in complex with its PI5P4Kα target.


  • Organizational Affiliation

    The ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building, Cambridge Biomedical Campus, Hills Road Cambridge CB2 0AH UK spa26@cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha375Homo sapiensMutation(s): 0 
Gene Names: PIP4K2API5P4KAPIP5K2PIP5K2A
EC: 2.7.1.149
UniProt & NIH Common Fund Data Resources
Find proteins for P48426 (Homo sapiens)
Explore P48426 
Go to UniProtKB:  P48426
PHAROS:  P48426
GTEx:  ENSG00000150867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48426
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U1U (Subject of Investigation/LOI)
Query on U1U

Download Ideal Coordinates CCD File 
B [auth A]~{N}-(3-chloranyl-4-methoxy-phenyl)-7-(3,4-dimethylphenyl)pyrrolo[2,3-d]pyrimidin-4-amine
C21 H19 Cl N4 O
DZIHITUUUPJMOQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.661α = 90
b = 84.935β = 90
c = 128.346γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references